Sept. 11 trial stumbles on documents so secret the judge can’t see them. For now.

In a bizarre new episode in the Sept. 11 trial, defense lawyers wrote a legal brief based on documents from the prosecution that are so far so secret the judge can’t see them.

Death penalty defender Jay Connell described the ongoing problem Monday at the opening of a weeklong pretrial hearing in the case against five men accused of conspiring in the Sept. 11, 2001, hijackings that killed nearly 3,000 people in New York, at the Pentagon and in a Pennsylvania field.

He said that he had sought starting June 7 to file a Top Secret legal pleading and 10 accompanying notices, supported by 5,000 pages of documents. But the court’s security officer would not take them because they had unfamiliar classification markings.

In them, based on court discussion, Connell appeared to be asking the judge to call certain experts and government witnesses on the question of when the war on terror began. Also, he appears to be seeking experts to testify on the reliability of post-torture interrogations in a bid to disqualify any confessions his client, Ammar al Baluchi, made to FBI agents soon after he got to Guantánamo in 2006.

Prosecutors who had provided Connell with the material in trial preparation were trying to figure out if the judge and his security staff need a security clearance to see it.

Connell was puzzled. If he, presumably had clearance to see the material, how could the judge not?

“As I understood the problem,” Connell said, “there’s the possibility that some of these compartments ... have been disestablished and the reason that the trial judiciary asked me to get the classification review was to find out, do these compartments still exist. If so, what is their current name so that they can seek a read-on for you or for me or for whoever.”

In this sketch by courtroom artist Janet Hamlin and approved for release by a Pentagon contractor, Khalid Sheik Mohammed, with his gray beard streaked with reddish-orange dye, attends an Aug. 19, 2013 pretrial hearing at the U.S. Navy Base in Guantánamo Bay, Cuba.

JANET HAMLIN Associated Press

The trial judge, Army Col. James Pohl, expressed similar bewilderment at an ongoing effort by prosecutors to figure out whether the judge and his staff had been cleared.

Attorney David Nevin, defending the alleged 9/11 plotter, said Khalid Sheik Mohammed was disturbed on Sunday to learn about the ongoing issue.

Nevin quoted Mohammed as telling him Sunday: “I’m used to the idea that they can kill me based on things I can’t see. But now it seems they want to kill me based on things the judge can’t see.”

Pohl expressed discomfort with the characterization “that somehow this case is going to be adjudicated with evidence that I don’t see. I don’t think that’s really going to happen.”

However, he noted, “Mr. Nevin did make a good point,” noting this was an “issue of a document being marked with a program that nobody’s aware of ... My office rejected it because we don’t know what the program is.”

Connell is the Pentagon-paid death-penalty defender of Mohammed’s nephew, Baluchi. The trial takes place in a maximum-security, eavesdrop-proof court compound where the public gets to hear the proceedings on a 40-second delay — in case someone divulges classified information that only those inside, with Top Secret clearances, can hear.

This is not the first time the case has stumbled over a clearance problem.

In October 2015, the judge required an intelligence agency authorization, known as a read-on, to receive some information as well. In this instance, the prosecution is working with the intelligence community to identify the programs or agencies responsible for classifying the information in Connell’s filings to determine what, if any, authorization the judge and his staff would need.